Competition between Na⁺ and Rb⁺ in the minor groove of DNA

The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration...

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Bibliographic Details
Published in:Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2012-05, Vol.85 (5 Pt 1), p.051913-051913, Article 051913
Main Authors: Shen, X, Atamas, N A, Zhang, F S
Format: Article
Language:English
Subjects:
Base Sequence
Binding, Competitive
DNA, B-Form - chemistry
DNA, B-Form - genetics
DNA, B-Form - metabolism
Molecular Dynamics Simulation
Nucleic Acid Conformation
Rubidium - metabolism
Sodium - metabolism
Temperature
Water - chemistry
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Summary:The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.
ISSN:1539-3755
1550-2376
DOI:10.1103/PhysRevE.85.051913